Mapping single atoms in biological structures is now becoming within the reach of analytical electron microscopy. Electron energy-loss spectroscopy (EELS) in the field-emission scanning transmission electron microscope (STEM) provides a particularly high sensitivity for detecting the biologically important element, phosphorus. Imaging can be performed at low dose with dark-field STEM prior to analysis at high dose, so that structures of macromolecular assemblies can be correlated with the numbers of specific atoms that they contain. Measurements confirm theoretical predications that single atom detection requires a nanometer-sized probe. Although phosphorus atoms may have moved several nanometers from their original positions by beam-induced structural degradation at the high required dose of ~109 e/nm2, damaged molecules are nevertheless stable enough to be analyzed at 1 or 2 nm resolution. Such analyses can only be achieved by means of spectrum-imaging with correction for specimen drift. Optimal strategies for mapping small numbers of phosphorus atoms have been investigated using well characterized specimens of DNA plasmids and tobacco mosaic virus. This technique should allow us to address a range of interesting biological problems such as the phosphorylation of proteins. It should also be possible to detect single atoms of other biologically important elements like calcium and iron that also have favorable ionization cross section. (This is a continuation of Intramural Research Project Z01-RR-10296-10 BEI.)